Abstract
Various strains of the mycoparasitic fungal species Clonostachys rosea are used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy of C. rosea in biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction between C. rosea and plant pathogenic fungi. Here, we determined the genome sequences of 11 Clonostachys strains, representing five species in Clonostachys subgenus Bionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p ≤ .05) in the Bionectria subgenus lineage. This was accompanied with gene copy number increases (p ≤ .05) in ATP‐binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. Most Clonostachys species were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose–methanol–choline oxidoreductases and additional carbohydrate‐active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of the C. rosea genome included expansions (p ≤ .05) of the ABC‐B4 multidrug resistance transporters, the ABC‐C5 multidrug resistance‐related transporters and the 2.A.1.3 drug:H + antiporter‐2 MFS drug resistance transporters. The ABC‐G1 pleiotropic drug resistance transporter gene abcG6 in C. rosea was induced (p ≤ .009) by exposure to the antifungal Fusarium mycotoxin zearalenone (1121‐fold) and various fungicides. Deletion of abcG6 resulted in mutants with reduced (p < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites in Clonostachys subgenus Bionectria.
Highlights
Parasitic interactions of a fungus on other living fungi involving penetration of host or prey hyphae are referred to as mycoparasitism (Barnett, 1963)
We hypothesized that factors contributing to efficient mycoparasitism and polyphagy should enable recognition and exploitation of C. rosea as a beneficial agent for controlling plant diseases in crop production
Identification of several presumed C. rosea strains as other Clonostachys species, together with C. solani, provided us with a suitable dataset to perform a comparative genomic investigation of Clonostachys subgenus Bionectria
Summary
Parasitic interactions of a fungus on other living fungi involving penetration of host or prey hyphae are referred to as mycoparasitism (Barnett, 1963). Certain species of Clonostachys and Trichoderma share an ecological role as generalists, being able to feed on multiple nutrient sources including live and dead fungi (mycotrophy) and dead plant or animal material (polyphagy) (Karlsson et al, 2018). Representatives of both genera are aggressive necrotrophic mycoparasites with a broad host range, including both alloparasitism (parasitism on unrelated hosts) as well as adelphoparasitism (parasitism on closely related hosts) (Druzhinina et al, 2011; Jensen et al, 2007). The approach allows to increase our understanding of the evolution of factors involved in mycoparasitism, plant beneficial traits and drug efflux in Clonostachys subgenus Bionectria
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